PoPoolation trimming pipeline

PoPoolationis a toolkit for handling Pool-Seq data, which includes a Perl script for performing a trimming pipeline similar to the one implemented here (trim-fastq.pl).

All features implemented in that script could be mimic in TrimReads to apply the same trimming pipeline.


The correspondence between arguments is the following:

PoPoolation TrimReads Note
Default Default ReadTools does not output single end in a separate file yet. This may be solved in the future
--no-trim-quality --disableTrimmer MottQualityTrimmer  
--min-length --minReadLength  
--no-5p-trim --disable5pTrim  
--quality-threshold --mottQualityThreshold  
--discard-internal-N --readFilter AmbiguousBaseReadFilter --ambigFilterFrac 0 This option is behaving slightly different. PoPoolation applies this filter before trimming the quality and TrimReads apply it afterwards